In the manga, Senjumaru did not employ Bankai. The character's abilities and actions were depicted differently without resorting to this particular power.
Shinji did use his Bankai in the manga. It was a crucial moment that turned the tide of the fight. The Bankai's power and unique abilities were showcased, adding an exciting element to the story.
In general, 'urahara x reader' fanfiction often focuses on the unique relationship between Urahara and the reader - inserted character. It might explore his mysterious nature and how the reader character interacts with it.
Yes, there are some. You can start by looking on fanfiction platforms like Archive of Our Own. There might be various stories exploring the unique relationship between Urahara and Spock, but the quantity might not be as large as more common crossovers.
It could start with a simple exchange of knowledge. Naruto teaches Urahara about chakra and ninjutsu, while Urahara shows Naruto some of his scientific breakthroughs. This mutual learning experience could bring them closer. They might start to understand each other's values and dreams, and over time, their bond could evolve into a loving relationship as they realize how much they have in common despite coming from different worlds.